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60 lines
2.1 KiB
Text
60 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf'
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include { DRAGMAP_ALIGN } from '../../../../modules/dragmap/align/main.nf'
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workflow test_dragmap_align_single_end {
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input = [
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[ id:'test', single_end:true ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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DRAGMAP_HASHTABLE ( fasta )
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DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
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}
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workflow test_dragmap_align_single_end_sort {
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input = [
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[ id:'test', single_end:true ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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DRAGMAP_HASHTABLE ( fasta )
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DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
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}
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workflow test_dragmap_align_paired_end {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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DRAGMAP_HASHTABLE ( fasta )
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DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
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}
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workflow test_dragmap_align_paired_end_sort {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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DRAGMAP_HASHTABLE ( fasta )
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DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
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}
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